by

Where communities thrive


  • Join over 1.5M+ people
  • Join over 100K+ communities
  • Free without limits
  • Create your own community
People
Activity
    Marius van den Beek
    @mvdbeek
    that I can find on the tool shed, and in the repo search on Galaxy
    revision 5 is the newest though — in the Galaxy interface
    can you open an issue about that ? guess we need to check the index and the repo metadata
    M Bernt
    @bernt-matthias
    Can do. Issue in the main Galaxy repo?
    Marius van den Beek
    @mvdbeek
    yes
    M Bernt
    @bernt-matthias
    @mvdbeek galaxyproject/galaxy#10324 .. got even more confusing after I inspected the logs which told me that revison 1 and 2 are installed (and not 1 and 5 as in the Admin UI)
    Marius van den Beek
    @mvdbeek
    which logs ?
    also which Galaxy version are you running ?
    M Bernt
    @bernt-matthias
    20.05 .. the galaxy log file
    Marius van den Beek
    @mvdbeek
    I don’t think that you have logs for revision 1 and 2 is a problem
    2 is not an installable revision anymore
    suite updates have never worked, as far as I can remember
    it is a problem though that Galaxy doesn’t show revision 6 as installable
    M Bernt
    @bernt-matthias

    OK. But why can't I find a trace of revision 5 in the logs ...

    I usually uninstall the suite (manually) and install the new revision which used to work so far ... I'm just to lazy to setup separate entries for tools collections with >100 tools (e.g. mothur and openms).

    Marius van den Beek
    @mvdbeek
    Maybe the update step doesn’t leave the same logs ?
    you mentioned you’re using https://github.com/galaxyproject/ansible-galaxy-tools … I don’t think that is maintained and is probably using outdated ephemeris versions ?
    Can you check in your repo in disk the hg revision ?
    (hg tip) ?
    M Bernt
    @bernt-matthias
    Can do.
    Marius van den Beek
    @mvdbeek
    also hg status might be interesting
    M Bernt
    @bernt-matthias
    Regarding the logs: Unfortunatelly the line Loaded tool id: toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_check/mothur_align_check/1.39.5.0, version: 1.39.5.0 into tool panel.... does not mention the hash
    Marius van den Beek
    @mvdbeek
    you mean the changeset revision ?
    M Bernt
    @bernt-matthias
    jep ...
    Marius van den Beek
    @mvdbeek
    and/or the path on disk ?
    feels like that would be overly verbose … might make more sense to add this in the admin panel ?
    or in the tool form in a way that only admins see it ?
    it’s already in the api if you look at /api/tools (for admins)
    M Bernt
    @bernt-matthias
    hg status shows me no output for shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_check/1d7284662c8b/mothur_align_check and shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_check/814a34469480/mothur_align_check which should be revisions 1 and 2 (and not 1 and 5 as shown as installed in the UI)
    Marius van den Beek
    @mvdbeek
    minor revision (=no tool bump) are just hg updated in their original location, so I’m not convinced the UI is wrong
    Marius van den Beek
    @mvdbeek
    hg tip should show you revision 5 (or maybe 6?)
    exposing all of these hg concepts to admins wasn’t a great idea … things looked very differently when the TS was written
    M Bernt
    @bernt-matthias
    indeed. changeset: 6:0399e5aeaac6 for /data/galaxy_server/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/mothur_align_check/814a34469480/mothur_align_check .. then just the admin UI display is wrong
    Marius van den Beek
    @mvdbeek
    I think the update may have just not finished before the database version was augmented
    that’s a little fragile on Galaxy’s side, but I would blame old ephemeris on this one
    M Bernt
    @bernt-matthias
    I'm using ephemeris==0.10.4 in the role
    which seems not to old
    Marius van den Beek
    @mvdbeek
    no, that’s the last version
    is this from a fork ? the master branch uses 0.8.0
    M Bernt
    @bernt-matthias
    I just updated it manually .. :| ..
    Marius van den Beek
    @mvdbeek
    pretty sure the role would overwrite this then, if by manually you mean just installing a newer version by hand
    it even sets upa temporary venv just for that task
    iirc
    M Bernt
    @bernt-matthias
    I changed it in the sources of the role
    Marius van den Beek
    @mvdbeek
    ok
    M Bernt
    @bernt-matthias
    Wondering how people install tools nowadays. I guess via the new mighty ansible roles .. unfortunatelly I never made to switch to them and got stuck in my self written ansible mess which I created before those became available
    which uses just ephemeris
    I don’t have to maintain a server anymore, but for my local needs I just mount usegalaxy.org’s toolset
    via cvmfs
    M Bernt
    @bernt-matthias
    Unfortunatelly I could not convince our admins to enable cvmfs :( .. but the scripts should be useful for my needs.